well, i have two disks in my old comp (60gb ibm [D:] and 15gb maxtor [C:])
the 15gb had win98 instaled and some important files. so, i didnt format it. i just used the boot disk to manualy deleet the win 98 files. then, i formated d: /s and installed windows. when it comes to the part where you have to choose the windows folder. i chose d:\win but after instaling i took a look at the c: drive and (to my surprise) the boot files like autoexec, etc remained there although win was installed on d: . If I change the booting device in the BIOS to HDD-1 then, after the verifying dmi pool data, it says "press any key to reboot" (even if i copy the boot files autoexec etc to drive d:

the prob is that i dont wan this because latter i wanna install linux to c:

well, once again remove windows files from c:, then disconnect it, making d: the master drive (remember to adjust the pins in back of HD accordingly), install 98 (d: will now become c: drive). re-attach the other drive as slave, install linux then either leave it as d: or switch pins around once again to make linux c: and 98 as d: